A late goal from Salomon Kalou proved the winner for the visitors.
Di Matteo said: "I think we've put ourselves in a good position, but it's not a result you can rely upon for the home game. It's one goal.
"You look at he results Benfica have achieved in this Champions League...you're not going to sleep very calmly looking at that.
"We are pleased that we're in a different position going into the second leg.
"We had a mountain to climb against Napoli. We still have a mountain, but it may be a little bit smaller because we've achieved a good result here."